Analysis of the algorithm: From kernels to backup genes.

Kernelization section

The algorithm transformed the semantic similarity matrix to make it compatible with a kernel. Once this was done for each network and kernel type, it was integrated by kernel type. Below there is a general analysis of the properties of each matrix in the different phases of the process.

Annotations properties

Table 1. Annotation files descriptors

Net Min Max Average Standard_Deviation
biological_process 1 134 6.9968818026710595 11.431432499773674
cellular_component 1 40 4.162222345933308 5.25157343549579
disease 1 21 2.2250479846449136 2.909050012799259
genetic_interaction 1064.0 1070.0 1069.7655871845109 1069.7662188776321
molecular_function 1 26 3.028670320161523 3.71561924352452
pathway 1.0 191.0 4.003825833485152 8.704590940604282
phenotype 1 335 31.549734094937957 46.988832336933186
protein_interaction 1.0 729.0 29.8386134923593 54.03869234947398

Matrix properties

Table 2. Similarity matrixes

Net Matrix_Dimensions Matrix_Elements Matrix_Elements_Non_Zero
biological_process_sim 16997x16997 288898009 259379720
cellular_component_sim 17963x17963 322669369 322651406
disease_sim 4168x4168 17372224 16578192
genetic_interaction_sim 17354x17354 301161316 1862674
interaction_sim 16098x16098 259145604 479348
molecular_function_sim 17335x17335 300502225 300484890
paper_coDep_sim 3365x3365 11323225 132458
pathway_sim 3828x3828 14653584 159182
phenotype_sim 5077x5077 25775929 25770852
protein_interaction_sim 16098x16098 259145604 479348

Table 3. Filtered similarity matrixes

Net Matrix_Dimensions Matrix_Elements Matrix_Elements_Non_Zero
biological_process_sim 16994x16994 288796036 259279570
cellular_component_sim 4129x4129 17048641 17044512
disease_sim 4008x4008 16064064 15325558
molecular_function_sim 7683x7683 59028489 59020806
pathway_sim 3423x3423 11716929 159134
phenotype_sim 4597x4597 21132409 21127812

Table 4. Uncombined kernel matrixes

Net Kernel Matrix_Dimensions Matrix_Elements Matrix_Elements_Non_Zero
biological_process ct 16997x16997 288898009 288898009
biological_process el 16997x16997 288898009 288898009
biological_process ka 16997x16997 288898009 259396717
biological_process rf 16997x16997 288898009 288898009
cellular_component ct 17963x17963 322669369 322669369
cellular_component el 17963x17963 322669369 322669369
cellular_component ka 17963x17963 322669369 322669369
cellular_component rf 17963x17963 322669369 322669369
disease ct 4168x4168 17372224 17372224
disease el 4168x4168 17372224 17355558
disease ka 4168x4168 17372224 16582360
disease rf 4168x4168 17372224 17355558
genetic_interaction ct 17354x17354 301161316 297804049
genetic_interaction el 17354x17354 301161316 293368612
genetic_interaction ka 17354x17354 301161316 1880028
genetic_interaction rf 17354x17354 301161316 293368612
molecular_function ct 17335x17335 300502225 300502225
molecular_function el 17335x17335 300502225 300502225
molecular_function ka 17335x17335 300502225 300502225
molecular_function rf 17335x17335 300502225 300502225
paper_coDep ct 3365x3365 11323225 11323225
paper_coDep el 3365x3365 11323225 9716415
paper_coDep ka 3365x3365 11323225 135823
paper_coDep rf 3365x3365 11323225 9716415
pathway ct 3828x3828 14653584 14432317
pathway el 3828x3828 14653584 8641524
pathway ka 3828x3828 14653584 163010
pathway rf 3828x3828 14653584 8641524
phenotype ct 5077x5077 25775929 25775929
phenotype el 5077x5077 25775929 25775929
phenotype ka 5077x5077 25775929 25775929
phenotype rf 5077x5077 25775929 25775929
protein_interaction ct 16098x16098 259145604 259081193
protein_interaction el 16098x16098 259145604 252047984
protein_interaction ka 16098x16098 259145604 495446
protein_interaction rf 16098x16098 259145604 252047984

Table 5. Integrated kernel matrixes

Integration Kernel Matrix_Dimensions Matrix_Elements Matrix_Elements_Non_Zero
integration_mean_by_presence ct 19635x19635 385533225 374538478
integration_mean_by_presence el 19635x19635 385533225 373204180
integration_mean_by_presence ka 19635x19635 385533225 350856728
integration_mean_by_presence rf 19635x19635 385533225 373204180
mean ct 19635x19635 385533225 374538478
mean el 19635x19635 385533225 373204180
mean ka 19635x19635 385533225 350856728
mean rf 19635x19635 385533225 373204180

Weight values